chemaxon.marvin.alignment

Class AlignOnPairedAtoms

java.lang.Object

chemaxon.marvin.alignment.AlignOnPairedAtoms

All Implemented Interfaces:

chemaxon.license.Licensable

public final class AlignOnPairedAtoms
extends Object

Overlays two molecules using the user defined atom pairs
Example:

 Molecule mRef = null;
 Molecule m = null;
 AlignOnPairedAtoms ap = new AlignOnPairedAtoms();
 ap.setReferenceMolecule(mRef, false); // reference will be kept rigid
 ap.setMoleculeToAlign(m, true); // this will be kept flexible
 // add pairs where you want
 for (int i = 0; i < m.getAtomCount(); i++) {
        p.addAtomPair(i, i);
 }
 ap.findFirst(); // aligns in the input conformation
 ap.findNext(); // randomizes the flexible molecules if flexible alignment
                                // selected and aligns.
 System.out.println("rmsd: " + p.getRmsd());
 Molecule result = p.getAlignedWithNewCoordinates();
 

Since:

marvin 5.2.3

Constructor Summary

Constructors

Constructor and Description
AlignOnPairedAtoms()

Method Summary

Methods

Modifier and Type	Method and Description
void	addAtomPair(int atom0, int atom1) Adds an alignment constraint between the reference and aligned molecule.
void	addAtomPair(int atom0, int atom1, double weight) Adds an alignment constraint between the reference and aligned molecule.
double	align()
void	findFirst() Overlays the molecule to align on the reference using the predefined atom pairs.
void	findNext() Randomizes dihedral angles of the input conformation for flexible molecules and aligns.
Molecule	getAlignedWithNewCoordinates()
double[][]	getCoordinatesOfAligned()
double[][]	getCoordinatesOfReference()
double	getMaxGradLimit()
Collection<AlignmentMolecule>	getMolecules()
chemaxon.marvin.alignment.NodeColor	getNodeColor()
AlignmentProperties.NodeType	getNodeType()
Molecule	getReferenceWithNewCoordinates()
double	getRmsd()
int	getStepLimit()
int	getTimeLimit()
boolean	isLicensed()
void	removeAllPairs() Removes all user defined atom pairs.
void	removeMolecules()
void	setAromatize(boolean arg0) Deprecated.
void	setConformerCount(int count)
void	setConvergenceLimit(double converg)
void	setDehidrogenize(boolean arg0) Deprecated.
void	setFlexibleRingRotatableBondCount(int arg0)
void	setFlexibleRingSize(int arg0)
void	setLicenseEnvironment(String arg0)
void	setMolecules(AlignmentMolecule reference, AlignmentMolecule toAlign)
void	setMoleculeToAlign(Molecule m, boolean flexible) Sets the molecule to align to the reference.
void	setNodeType(AlignmentProperties.NodeType arg0)
void	setProgressMonitor(MProgressMonitor arg0)
void	setProperty(AlignmentProperties arg0)
void	setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType arg0)
void	setReferenceMolecule(Molecule m, boolean flexible) Sets the reference molecule to align to.
void	setStepLimit(int arg0)
void	setTimeLimit(int arg0)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AlignOnPairedAtoms

public AlignOnPairedAtoms()

Method Detail

removeMolecules

public void removeMolecules()

setReferenceMolecule

public void setReferenceMolecule(Molecule m,
                        boolean flexible)
                          throws chemaxon.marvin.alignment.AlignmentException

Sets the reference molecule to align to. All previously added molecules are removed.

Parameters:

m - reference molecule

flexible - if true treat this molecule flexible. If false its conformation is frozen.

Throws:

AlignmentException

setMolecules

public void setMolecules(AlignmentMolecule reference,
                AlignmentMolecule toAlign)

setConformerCount

public void setConformerCount(int count)

setMoleculeToAlign

public void setMoleculeToAlign(Molecule m,
                      boolean flexible)
                        throws chemaxon.marvin.alignment.AlignmentException

Sets the molecule to align to the reference.

Parameters:

m - this molecule will be translated and rotated

flexible - if true treat this molecule flexible. If false its conformation is frozen.

Throws:

AlignmentException

getCoordinatesOfReference

public double[][] getCoordinatesOfReference()

getCoordinatesOfAligned

public double[][] getCoordinatesOfAligned()

getReferenceWithNewCoordinates

public Molecule getReferenceWithNewCoordinates()

getAlignedWithNewCoordinates

public Molecule getAlignedWithNewCoordinates()

addAtomPair

public void addAtomPair(int atom0,
               int atom1,
               double weight)
                 throws chemaxon.marvin.alignment.AlignmentException

Adds an alignment constraint between the reference and aligned molecule. Both molecules must be added beforehand.

Parameters:

atom0 - atom seq starting from 0 from the reference molecule

atom1 - atom seq starting from 0 from the other molecule

weight - weight of the constraint of this pair

Throws:

chemaxon.marvin.alignment.AlignmentException - if there is no such atom

addAtomPair

public void addAtomPair(int atom0,
               int atom1)
                 throws chemaxon.marvin.alignment.AlignmentException

Adds an alignment constraint between the reference and aligned molecule. Both molecules must be added beforehand.

Parameters:

atom0 - atom seq starting from 0 from the reference molecule

atom1 - atom seq starting from 0 from the other molecule

Throws:

chemaxon.marvin.alignment.AlignmentException - if there is no such atom

findFirst

public void findFirst()
               throws chemaxon.marvin.alignment.AlignmentException

Overlays the molecule to align on the reference using the predefined atom pairs.

Throws:

AlignmentException

findNext

public void findNext()
              throws chemaxon.marvin.alignment.AlignmentException

Randomizes dihedral angles of the input conformation for flexible molecules and aligns. If only rigid molecules selected does nothing.

Throws:

AlignmentException

align

public double align()

getRmsd

public double getRmsd()

Returns:

the root mean square deviation of the current orientation of the two molecules.

removeAllPairs

public void removeAllPairs()

Removes all user defined atom pairs.

setConvergenceLimit

public void setConvergenceLimit(double converg)

setProperty

public void setProperty(AlignmentProperties arg0)

getMaxGradLimit

public double getMaxGradLimit()

getNodeType

public AlignmentProperties.NodeType getNodeType()

getNodeColor

public chemaxon.marvin.alignment.NodeColor getNodeColor()

setAromatize

@Deprecated
public void setAromatize(boolean arg0)

Deprecated.

setDehidrogenize

@Deprecated
public void setDehidrogenize(boolean arg0)

Deprecated.

setFlexibleRingSize

public void setFlexibleRingSize(int arg0)

setFlexibleRingRotatableBondCount

public void setFlexibleRingRotatableBondCount(int arg0)

getMolecules

public Collection<AlignmentMolecule> getMolecules()

isLicensed

public boolean isLicensed()

Specified by:

isLicensed in interface chemaxon.license.Licensable

setLicenseEnvironment

public void setLicenseEnvironment(String arg0)

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

getStepLimit

public int getStepLimit()

setStepLimit

public void setStepLimit(int arg0)

getTimeLimit

public int getTimeLimit()

setNodeType

public void setNodeType(AlignmentProperties.NodeType arg0)

setTimeLimit

public void setTimeLimit(int arg0)

setProgressMonitor

public void setProgressMonitor(MProgressMonitor arg0)

setProximity

public void setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType arg0)